Principles of Taxonomy and Classification: Current Procedures for Naming and Classifying Organisms Michael Ohl Contents Introduction ...................................................................................... 214 Definitions ....................................................................................... 215 Taxonomy as a System of Ordering Data ...................................................... 218 Taxonomy and Classification Without Phylogeny: An Outdated Remnant or a Practical Necessity? ....................................................................................... 219 Zoological Nomenclature: Governing the Process of Naming .. .............................. 221 Ranking Hierarchies: Capacity and Limits of Linnaean Categories ....................... 222 The International Code of Zoological Nomenclature ...................................... 227 Conclusion ....................................................................................... 233 Cross-References ................................................................................ 234 References ....................................................................................... 234 Abstract Taxonomy deals with the naming and classification of organisms and is an integrative part of biological systematics, the science of biodiversity. The information provided by taxonomic research is a fundamental basis for all fields of biology. Current taxonomy focuses on multicharacter integrative approaches, considering all potentially useful sources of information provided by the various fields of biology. The resulting supraspecific classification should be based on the genealogy of organisms, that is, on a phylogenetic analysis, to be objectively testable. However, for pragmatical reasons, a classification based on overall similarity and diagnostically relevant characters might be a heuristically impor- tant step in taxonomy and should be perceived as an approximation to a M. Ohl (*) Museum fur€ Naturkunde - Leibniz-Institut fur€ Evolutions- und Biodiversita¨tsforschung, Museum fur€ Naturkunde, Berlin, Germany e-mail: [email protected] # Springer-Verlag Berlin Heidelberg 2015 213 W. Henke, I. Tattersall (eds.), Handbook of Paleoanthropology, DOI 10.1007/978-3-642-39979-4_4 214 M. Ohl classification tested by phylogenetic methods. The nested levels in a classifica- tion of organisms are usually not only named but also ranked, that is, a set of hierarchical terms, like genus, family, and class, is applied to reflect the hierar- chical structure of the classification. Assigning these so-called Linnaean cate- gories to a classification is (1) a voluntary action to make a classification notionally more easy to access and (2) a linguistic activity that is done subse- quent to obtaining the scientific results of the systematic analysis. Introduction Taxonomy, the science and method of naming organisms, is a fundamental basis for all biological science and its application (Sluys 2013). The primary task of taxon- omy is to describe, establish, and give an account of the order that is an inherent property of biological diversity. The order of names provided by taxonomy is arranged as a hierarchical classification, which is considered to portray the hierar- chy of species and more inclusive taxa as a result of the continuous chain of species splittings in the evolutionary history of life on earth. Generalizations on organisms as a basic principle in biology are only possible if the infinite number of items in science is classified. Statements about the overwhelming diversity of nature would be impossible without methods for bringing order to this diversity. The world’s biota is a vast library of information concerning any aspect of life, and taxonomy is the cataloguing system that everybody must use to access its information. All kinds of biological science and applications link their specific data to species names and use these names for effective communication. As Longino (1993, p. 85) has paraphrased, “...taxonomy is the raw material from which hypotheses of phylog- eny are derived.” All kinds of comparative biology rely on sound phylogenetic hypotheses, and the reliability of a phylogenetic hypothesis immediately depends on the reliability of the underlying taxonomic data. Moreover, society has an increasing need for reliable taxonomic information in order to allow to manage and understand the world’s biodiversity (Wheeler et al. 2004; Costello et al. 2013). Until recently, taxonomy was confronted with what Godfray (2002, p. 17) called a new bioinformatics crisis, evidenced “by a lack of prestige and resources that is crippling the continuing cataloguing of biodiversity.” Current biological taxonomy quite successfully adopts methods, data structure, and other demands of techniques and theories invented by new entrants to the biological sciences such as the fields of molecular biology (e.g., DNA barcoding; see De Salle et al. 2005). However, all other useful sources of information are simultaneously gathered in modern taxon- omy, and this multicharacter integrative approach has been called integrative taxonomy (Dayrat 2005; Wheeler 2005; Padial et al. 2010). It allows taxonomists to create new common visions to meet changing demands of a changing global view on global biodiversity and the threats to it (Wheeler and Valdecasas 2005; Wheeler 2008; Polaszek 2010; Wheeler et al. 2012). Principles of Taxonomy and Classification: Current Procedures for Naming and... 215 Definitions Inconsistent terminology is a barrier to communication, results in confusion and misunderstanding, and prevents effective science. The variation in definitions for “taxonomy,” “systematics,” “classification,” and related or derived terms is as complex as it is contradictory. The major problem with these obviously closely allied terms is to differentiate them from each other, and many authors treat them more or less as synonyms, either intentionally or intuitively. In a recent textbook on biological systematics, Schuh (2000) implicitly equated systematics, classification, and taxon- omy, when he defined systematics as “the science of biological classification.” The opposite view is held by Hawksworth and Bisby (1988, p. 10), who suggested restricting taxonomy to “taxonomic information systems (classification, nomencla- ture, descriptions, identification aids)” and defining systematics to include “taxon- omy in the above restricted sense together with analyses of variation, of phylogeny, evolutionary processes, etc.” Probably, most current scientists would agree that the most appropriate name for the scientific area composed of taxonomy, systematics, classification, and all of their respective concepts, theories, and methods is “biological systematics,” or systematics in short. What are the basic units of systematics? Systematics is not concerned with individual organisms, although these are always studied by systematists as repre- sentatives of species or other supraspecific groupings. The simplest and most descriptive statement would be that systematics deals with taxa. What then is a taxon (plural, taxa)? Simpson (1961, p. 19) defined it as “a group of real organisms recognized as a formal unit at any level of a hierarchic classification.” This definition recognizes groups of organisms as taxa only if they are already formally classified, which is not always necessary or wanted. Newly discovered groups, hypothetical groups that still await confirmation, putatively artificial groups that are still disputed, and many others do not qualify as taxa under Simpson’s definition. In the field of phylogenetic systematics or cladistics, the taxon definition is often narrowed even further to monophyletic groups of organisms (Sudhaus and Rehfeld 1992; Mayr and Bock 2002). The final objective of systematics is indeed to include monophyletic groups only, but for a wide variety of reasons, this goal can hardly be achieved right away. Hypotheses on monophyly are created and rejected, groups prove to be nonmonophyletic but are still being discussed, and putatively mono- phyletic groups are still of unknown position within a certain higher lineage. Other problematic cases are fossil stem groups, like Australopithecinae, which are obvi- ously paraphyletic with respect to Hominidae but can be treated as a heuristically important grouping in paleoanthropology. All these groupings are best referred to by a generalized term, and taxon is the most appropriate one. Hence, a definition of the term taxon might be: “A taxon is a group of organisms that can be differentiated from other groups of organisms, and that can be described and named.” Other terms to replace the term taxon have been proposed that are considered to carry specific connotations to reflect a specific framework for which they have been proposed. 216 M. Ohl Terminal taxon, as used in cladistics, and operational taxonomic unit (OTU), proposed by the phenetic school of systematics, are two prominent examples that have been suggested to designate the units of systematics without reference to a particular rank or phylogenetic position. However, the term taxon, as here defined, is sufficient to refer to ranked and unranked groups of organisms. Biological systematics in fact deals with taxa, that is, biological populations, species, and higher taxa. However, systematics is concerned not only with the taxa themselves and their description and characterization but also with their origin, development, and other kinds of interrelationships. The fundamental and underly- ing concept